ratePvals: Retrieve a single p-value for each rate

Description

Retrieve a single p-value for each rate

This method is used to retrieve all the p-values combined with Brown's method that combines the results of the
log likelihood ratio test results for all pairs tested for each rate and all genes. P-values will change
according to the threshold set for the chi-squared test because it influences the model that will be taken into
consideration to perform log likelihood ratio tests. To have a sense of the best parameter to choose, a sythetic
data-set can be built and tested (makeSimModel, makeSimDataset)
In case 'aic' has been selected via modelSelection method,
this method assigns the chi-squared test result of the model selected by AIC
to the respective variable rates

Usage

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Arguments

object

An object of class INSPEcT or INSPEcT_model

cTsh

A numeric representing the threshold for the chi-squared test to consider a model as valid

Details

ratePvlas retrieve a single p-value for each rate thanks to multiple log likelihood tests performed on
nested models that has a chi-squared test below the selected threshold.
Among the many p-values that log likelihood ratio test calculate, a single p-value is obtaied applying Brown's method
for combining dependent p-values.

Value

A matrix containing p-values calculated for each rate

See Also

Examples

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nascentInspObj10 <-readRDS(system.file(package='INSPEcT','nascentInspObj10.rds'))ratePvals(nascentInspObj10)# calculate agin the p-values with Brown with a different threshold # for considering a model valid for the log likelihood ratio testratePvals(nascentInspObj10, cTsh=.2)# Set permaenently the chi-squared threshold at .2 for nascentInspObj10 objectthresholds(nascentInspObj10)$chisquare <-.2